The JSpecView Project: an Open Source Java viewer and converter for JCAMP-DX, and XML spectral data files

The JSpecView Open Source project began with the intention of providing both a teaching and research tool for the display of JCAMP-DX spectra. The development of the Java source code commenced under license in 2001 and was released as Open Source in March 2006. The scope was then broadened to take advantage of the XML initiative in Chemistry and routines to read and write AnIML and CMLspect documents were added

A simpler method of preprocessing MALDI-TOF MS data for differential biomarker analysis: stem cell and melanoma cancer studies

<p>Abstract</p> <p>Introduction</p> <p>Raw spectral data from matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) with MS profiling techniques usually contains complex information not readily providing biological insight into disease. The association of identified features within raw data to a known peptide is extremely difficult. Data preprocessing to remove uncertainty characteristics in the data is normally required before performing any further analysis. This study proposes an alternative yet simple solution to preprocess raw MALDI-TOF-MS data for identification of candidate marker ions. Two in-house MALDI-TOF-MS data sets from two different sample sources (melanoma serum and cord blood plasma) are used in our study.</p> <p>Method</p> <p>Raw MS spectral profiles were preprocessed using the proposed approach to identify peak regions in the spectra. The preprocessed data was then analysed using bespoke machine learning algorithms for data reduction and ion selection. Using the selected ions, an ANN-based predictive model was constructed to examine the predictive power of these ions for classification.</p> <p>Results</p> <p>Our model identified 10 candidate marker ions for both data sets. These ion panels achieved over 90% classification accuracy on blind validation data. Receiver operating characteristics analysis was performed and the area under the curve for melanoma and cord blood classifiers was 0.991 and 0.986, respectively.</p> <p>Conclusion</p> <p>The results suggest that our data preprocessing technique removes unwanted characteristics of the raw data, while preserving the predictive components of the data. Ion identification analysis can be carried out using MALDI-TOF-MS data with the proposed data preprocessing technique coupled with bespoke algorithms for data reduction and ion selection.</p

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

CHEMSPIDER – BUILDING A STRUCTURE CENTRIC COMMUNITY FOR CHEMISTS

The task of finding chemical information online can be daunting, since even the most rudimentary query on Google can provide tens to hundreds of thousands of links to peruse. While there has been an increase in the number of online chemical structure databases (for example, PubChem), there has not been a central online resource allowing integrated chemical structure-searching of chemistry databases, chemistry articles, patents and web pages such as blogs and wikis until now. ChemSpider has built a structure centric community for chemists by providing free access to an online database and collaboration tool that offers an environment for curation of the data as well as the deposition of chemical structures, spectra and other analytical data and associated information. This provides a significant knowledge base and resource for chemists working in different domains. At present, there are over 20 million compounds indexed in ChemSpider and this is steadily growing with new information added daily. From an IUPAC perspective, this project can be considered to be a significant success story since ChemSpider has used both InChI and InChIkeys for development of the database and the provision of fast searching routines. ChemSpider has provided web services for both InChI generation and searching, leading to a proliferation of InChI’s in the web-based domain of chemistry. With the ability to deposit and view analytical data online, ChemSpider has depended on JCAMP-DX spectra data formats for display of spectra and utilized JSpecView as their viewing tool. An overview of present and future capabilities will be given

Equilibria in complexes of N-heterocyclic molecules. Part 29. An electron spin resonance study of some N-heterocyclic complex ions of silver(II)

A critical assessment of the e.s.r. parameters for complex compounds of the silver(II) ion with the N-heterocyclic donors pyridine, 2,2′-bipyridyl, and 1,10-phenanthroline is presented. In previous reports, nitric acid has often been used as an ‘inert’ solvent; this is wrong. Protons and silver(II) ions compete for the ligands, equilibria being fairly rapidly established. Species studied in nitric acid solutions made from solid compounds of silver(II) are usually not those present in the pure solid. Another important difference in the present investigation is in the assignment of the nitrogen superhyperfine coupling constants. It is now well established that A∥N and A⊥N cannot be immediately obtained from the e.s.r. spectra. This paper also introduces the use of a new line-sharpening device, suitable for obtaining extremely well resolved e.s.r. spectra of solids

Chemical markup, XML, and the world wide web. 7. CMLSpect, an XML vocabulary for spectral data

CMLSpect is an extension of Chemical Markup Language (CML) for managing spectral and other analytical data. It is designed to be flexible enough to contain a wide variety of spectral data. The paper describes the CMLElements used and gives practical examples for common types of spectra. In addition it demonstrates how different views of the data can be expressed and what problems still exist